All smooks configuration parts have an associated configuration namespace, which is declared in a namespace/prefix declaration on the root element of the configuration. These namespace declarations get added when a specific config type is added to the configuration e.g. a prefix:namespace declaration for the "http://www.milyn.org/xsd/smooks/freemarker-1.1.xsd" namespace is added when a FreeMarker config is added.
If all the configurations from a specific namespace are removed, so should the declaration for that namespace.